The Chaos Trapped Within
by natattack-alex
Summary: This was the first fan fiction I had ever written and thus it is the first I decided to publish onto this site. This is a few years old now. I hope you enjoy reading it, as much I enjoyed writing it. ;) Credits: -Alex and Nate the hedgehogs are characters of mine -Sonic and other characters belong to, well Sega and Archie Comic. Rate and Review please! Like it or hate it?
1. Prologue Parts 1 and 2

**Intro: Part 1**

Alex was only 8 years old when she had lost her parents to the war. Though she was young, she could sense that something was wrong when her grandparents spoke in hushed tones at dinner one night. Finally they turned to her and spoke.

"Alex, my dear, we have a bit of bad news for you. You know your parents were very brave, but I'm sorry to say that they have passed away."

She silently stared at them and then hopped off her chair. She ran to her room and grabbed her jacket and slipped on her shoes.

"Alex?"

She could hear the voice of her grandmother approaching. She quickened her haste, and then sprinted out the bedroom door. She ran past her grandmother in the hallway.

"Alex where are you…"

She was already out the door. She didn't realize that those would be the last words she would hear from her grandmother as she ran into the night.

_"Don't worry sweetie, we will be back. You'll know when that time comes. You'll feel it in your heart. And when you do, we'll be here waiting for you…"_

It had been 4 years since she had heard those words. The night grew cold around her as she ran through Mobotropolis. Finally she stood in front of an abandoned apartment building. As she stepped over the threshold her heart felt empty. That wasn't a good sign.

"Mom? Dad? Are you here?"

She looked around in the darkness, hoping to detect any sign of life.

"Mo..m? Da..d?"

Her eyes filled with tears and she sank to the floor.

"You said you would come back! You said you would be here! You didn't keep your promise! You lied!"

She covered her eyes and cried. Where was she going to go? She couldn't go back to her grandparents. They were slowly coming to end of their lives and raising her would just be a burden. She had no one.

**Part 2**

_A week later…_  
Roaming Mobotropolis seemed to be the only thing that Alex could do to entertain herself. She had taken shelter in the old apartment building, but there was nothing to do in there.

One night, as she made her way back to the building, she looked up to see someone running towards her. It was a young boy, about her age, and he looked worn out and tired. When he finally reached her he crouched down and put his hands on his knees, trying to catch his breath.

"Please help…."

The boy fainted before he could say his last word. Alex jumped and caught him before he hit the floor. She tried to carry him but failed, so she slowly dragged him to rest of the way to her apartment. When she reached, she pulled him into her bedroom and laid him on her mattress. She placed a warm rag on his forehead, and awaited his awakening.

"….where am I?"

Alex was awakened by the voice of the stranger that had fainted in front of her last night. She sat up and looked at him. He was covered in bruises and scratches.

"What happened to you? Why were you looking for help?"

He stuttered with his reply, as he held back tears.

"…they took my parents. They took them and turned them into robots!"

He choked on the words. Alex didn't know how to reply. She had also lost her parents, but not in the same way. She didn't know which was worse. Dying in the war against Robotnik, or being transformed into a robot to serve the enemy.

"I also lost my parents. They died in the war."

The boy looked up at her and then looked down again.

"I'm sorry."

"It's ok. They died for a good cause."

Alex refused to cry. She vowed to be as strong as her parents and one day grow up and become part of the resistance. Crying was a sign of weakness.

"Do you have any other family?"

The boy shook his head as he wiped his eyes dry.

"Well, you could stay here if you'd like. It's just me here, and as you can see I don't take up much room."

The boy smirked and looked at her. He then looked around. It wasn't exactly what someone would call "home" but it would do. At least he wouldn't be alone.

"Ok, I'll take you up on your offer. My name is Nate, by the way."

"Nice to meet you. My name is Alex."


	2. Prologue Parts 3 and 4

**Intro: Part 3**

_One year later…_

Mobotropolis had transformed into Robotropolis. It was no longer safe to live in the city unless you had submitted yourself over to Robotnik. Alex and Nate had safely fled the city, but now were roaming along the countryside. They were tired and hungry, but continued walking, hoping to find help. They entered the Great Forest, and as they traveled deeper into it, they were amazing to find civilization. They had reached Knothole Village.

"…so this place really exists?"

Alex stepped down the path and slowly entered they village. Her mother and father used to tell her that whenever she was in need of help she would always be welcomed here. She hoped that even though they were gone, that the "welcome" they spoke of still applied.

"What is this place?"

Nate had never heard of such a place.

"It's a refuge and base for the resistances against Robotnik. Follow me."

Alex had never been to Knothole, but it strangely felt like home. She looked around hoping to see a familiar face, and finally found one.

"...Mr. Stripe..?"

The tiger turned around to respond to his name.

"Yes? May I help you...?"

He looked at Alex and gasped.

"Alex?! Your alive?!"

He grabbed and embraced her.

"We were deeply saddened to discover that we had lost your parents during battle. Your grandparents contacted us and told us that you had run away, but that was a year ago."

Alex nodded. She looked around at the village.

"This is my friend Nate. We escaped Mobotropolis after it was captured, and have been traveling ever since."

"Well we should get you settled then," Mr. Stripe replied, "Welcome to your new home."

**Part 4**

_Two weeks later..._

Alex felt that she once again had a home. She and Nate had also made new friends with the other kids in the village including Sonic, Sally, Tails and Knuckles when he made his trip from Angel Island to visit. They all underwent training, and this is where Nate discovered that he had powers of Echolocation. He could sense the location of people or objects by using reflected sound waves, either given off the person or object. He could hear the faintest of sounds, even if it had happened a mile away.

"How annoying, there is nothing interesting about being able to hear a pin drop."

Alex laughed and padded him on the shoulder.

"That's not the only thing you can do. That power of yours could really come in handy in war."

"Yeah, I agree," Sally said as played around with her communicator, "We would be able to hear the plans of the enemy and still be at a safe distance from them."

"Humm," Nate thought. "I guess you're right. I never thought of it like that."

With that, Nate left the hut and ventured off the find the guys. Alex stayed with Sally as she tried to upgrade her communicator.

"Have you ever wished you had powers?"

"Who? Me?" Sally tapped her chin and shrugged. "I don't know. I always thought that as long as I did what I could to help out I would be considered a hero. I didn't need powers like Sonic or Nate."

"But it gives them a huge advantage," Alex said as she slumped down in the chair and rested her head in the palm of her hand.

"Not just them," Sally said sitting down next to her, "It gives our team a huge advantage. We are a team and there is no I in team. We all work together, so their powers aid all of us."

Alex nodded. "Your right."

"Now let's get out of here," Sally said. "I hate being trapped in the lab for so long. Let's go find the guys."

They both left the hut that they used as a laboratory and ran into the afternoon in search of the boys.

_What you are reading here is not the story. The story begins 9 years from now, after the Knothole Freedom Fighters successfully defeated Robotnik and restored Mobotropolis. All is well until a new enemy rises to the challenge of conquering the world. And now our story will begin. Unleash the Chaos trapped within._


	3. Chapter 1

**Chapter 1**

_We are now 9 years into the future. Alex and Nate are both now 18 and living in an apartment in New Mobotropolis._

_"…the city is crumbling to the ground. People are trying to flee. The world is in complete and total chaos. And then a bright light…_"

Alex's eyes opened.

"Not again," she said as she rubbed her forehead.

Ever since Alex had turned 18, she had been having a strange dream of the world coming to an end. But the odd part of the dream was that she could never get past the bright light scene. She would always wake up, and when she tried to close her eyes and continue the dream, all was lost.

"What does the dream even mean?"

She quietly got out of her bed and walked to the door. She opened it as quietly as she could and tiptoed passed Nate's bedroom.

"Who am I kidding?", she thought, "He could probably hear when I woke up."

And of course she was right. Nate's acute sense of hearing allowed him to hear anything miles away. Just hearing her tiptoe passed his room was like hearing thunder during a rainstorm. Although Alex knew this she continued to tiptoe until she reached the kitchen. She then opened one of the cupboards and grabbed a glass.

"I don't know why you even try," Nate said as he turned on the lights.

"Jeez! Don't sneak up on me like that!" Alex yelled as she jumped from being startled.

"Sorry," Nate said yawning and stretching. "So let me guess, you had the dream again?"

Alex sighed. "Yeah", she said as she turned on the faucet and filled the glass with water.

"And you didn't get passed the bright light part?", Nate asked and he helped himself to a glass of water as well.

"What do you think?", Alex replied, somewhat irritated about the matter.

"Relax, will you", Nate was slipping the water from his glass.

"I can't , I just want to know what the dream means and what it has to do with me."

She stopped drinking and poured the rest of the water down the sink. She began to head back to her room and walked passed Nate.

"Hey", he grabbed her wrist, "I know it must be hard for you, and I know you want answers, but you're going to have to be patient."

"Yeah", Alex sighed and turned her back, "I know."

She walked back to her room and closed the door behind her. Nate finished his water and turned off the lights. As Nate walked into his room he could hear Alex's soft breathing as she tried to fall back asleep.

"I'm sorry Alex. I wish I could help you more…"

The next morning Alex woke up to the sound of pots and pans being banged against the kitchen counter.

"Oh no", she thought, "He's attempting to cook."

She quickly jumped out of bed and got dressed fast. She swung her door open and ran out into the kitchen.

"Am I too late?"

"What's that supposed to mean?", Nate asked crossing his arms against his chest.

"Uhhhh", Alex scratched her head as she thought of an excuse that wasn't too harsh.

"I'm an amazing…",Nate sniffed the air and smelled something burning. "NO! That's the 3rd batch that's burned!"

Alex palmed her head as Nate scurried to turn off the stove.

"Ok, I give up", Nate said, surrendering the apron. "You can make breakfast today."

"Nate", Alex began as she tied up her hair, "I make breakfast every day."

"Yeah yeah, don't rub it in", Nate said as he sat down at the table. "I just thought it would be nice if I just tried every once in awhile."

"Nate", Alex began again as she raised an eyebrow, "You try every day."

"Whatever", Nate pouted.

_Somewhere on the outskirts of town in an old, abandoned factory…_

"This is our subject."

A dark figure handed a Chameleon a photograph. It was of a female hedgehog, about 4'7" with pale green fur and teal colored hair. The Chameleon nodded and put the photo in his pocket.

"Bring her back to me alive. If she is lost we'll be losing something very valuable."

"Yes master."The Chameleon bowed, camouflaged, and disappeared.


	4. Chapter 2

**Chapter 2**

"This really has to stop" Alex grumbled as she picked up a carton of eggs. This had been her 3rd time grocery shopping this week because of Nate's "experiments". Today she was accompanied by Amy, who would never pass up an opportunity to shop.

"Why don't you just show him how to cook?"

"I've tired, multiple times."

"Then there really is no hope for him is there?"

They both laughed as they finished their grocery shopping and left the market.

"So how's chasing Sonic going?"

Alex could never forget about Amy's massive crush on Sonic. She remembered how awkward it was when Sonic and Sally flirted in Amy presence during missions. And not just Sally, Mina as well, and sometimes even her. How could she ever forget the occasional "arm around the shoulder" hug?

"Same ol', same ol'", Amy shrugged "It keeps me fit running after him so I don't mind."

"You always find a way to make it seem fine" Alex sighed.

"What's wrong with that?" Amy protested, "You should always look for the good in things."

"Whatever you say."

"And speaking of running after boys, what's going on between you and Nate?"

Alex blushed. "Absolutely nothing!"

"Oh come on, you two live together."

"So what!?" Alex tried hard to defend herself, "What's wrong with two good friends living together?"

"Fine, fine", Amy waved her hand, "If you say so. But I'm telling you, there is something there."

Alex shook her head. It was like Amy to bother her about stuff like this. Sally was the same as well. It seemed like all the girls believed that there was something between her and Nate, when such a thing didn't exist. It had been 9 years since they had met and they were more like brother and sister. But although she thought this, she couldn't help but sometimes wonder what it would be like if she and Nate were more than friends. They did have a lot in common and knew almost everything about each other.

"Well this is my stop." Amy waved goodbye and walked down the block.

Alex continued to her apartment. It was early evening and the sun was setting. The streets were somewhat empty and quiet.

"Better get home fast before Nate uses up whatever's left."

As she walked she couldn't help but feel as if she was being followed. She turned to look but saw no one. She turned back around and quickened her pace.

"What is wrong with me? There is nothing behind me yet I feel so strange."

And then she felt something. An arm grabbed her and tried to pull her aside into an alley. She fought this invisible force with all her might, wondering if anyone was noticing that she was punching the air. Throwing her fists about paid off however, when they came in contact with what felt like a cheekbone. The being that was once invisible came into view. It was a chameleon, dressed entirely in black.

"Submit to me and I will cause you no harm."

"As if!"

Alex kicked him, and dashed down the block. She was only a few feet away from her building, so she looked back. The chameleon had vanished. Breathing heavily she walked up the steps and through the door. When she reached her apartment door she stopped to take a breath.

"What was that all about?"

She reached into her pocket for her key and unlocked the door. She stepped in, closed the door, and leaned against it trying to re-catch her breath.

"What happened to you?"

Nate stepped into the hallway, holding the apron in his hand. Alex, who was not in the mood to be interrogated, ran, grabbed the apron and turned into the kitchen.

"I was worried you would try something like this", she reply shaking the apron in front of him. He pouted and left the kitchen. Alex smirked, tied the apron around her waist, and began to prepare dinner.


	5. Chapter 3

**Chapter 3**

Days had passed since Alex had been attacked near her apartment. That didn't stop her from venturing out however. She was a Freedom Fighter, and nothing scared her after all those crazy missions to above and beyond. But she still didn't understand why she was the one being targeted.

"What to do today?"

Everyone was busy today. Amy had a hair appointment, Sally was visiting her father, Sonic was on one of his runs, Tails had locked himself in his lab, and Nate was busy meditating. Alex knew better than to interrupt Nate while he was doing Sonar exercises. Master Long told him that if he practiced daily, he could increase his powers, and Nate had nothing against getting stronger.

"Are you done? You're wasting daylight!" Alex said impatiently. Nate ignored her. He had more control over his powers that he could even block out sounds that he didn't want to hear, for example: Alex's nagging.

"Are you tuning me out?!"

No reply.

"Fine, if you're going to play that game…" Alex grabbed her jacket and left. Nate, still tuning out unnecessary noise, did not hear the door slam shut.

Alex aimlessly walked through town. She thought about how she had treated Nate and felt bad, so she promised herself that she would apologize when she returned. Recently her patience level had gone down, due to the constant dreaming and the attack. She saw no connection between the two, so in additional to still being in the dark, she had even more questions.

"Hey, Alex!" Mina Mongoose waved. Being a celebrity, Mina always had to keep a low profile while she was out in town. She was now wearing sweats and sunglasses to hide her face. Alex couldn't help but laugh.

"What are you wearing?" Alex giggled as Mina strut towards her.

"What do you mean?", she replied, "I always wear this."

"Not during your concerts you don't."

"Shhhhh! Hey, I'm trying not to attract attention." Mina adjusted her glasses and looked around.

"Don't be so paranoid."

"Anyways, changing the subject, what's up?"

"Nothing new with me", Alex lied. She didn't feel like being a burden to anyone by complaining so she kept her latest news to herself. She was somewhat relieved though. Having Mina to hang out with now would keep her mind off of what was going on.

"How's Nate been?", Mina asked as they walked towards the town square.

"He's fine", Alex replied, "I left him to do his meditating." They stopped to eat lunch, walked around for a bit, and then parted ways.

Alex was quick to get home. She didn't feel like being held up like she been the other day, plus she wanted to be on good terms with Nate. As she stepped into the apartment she didn't hear the usual banging of pot and pans. Instead she just heard the soft buzzing of the television.

"Hey", Alex greeted him as she leaned on the door frame, "Have you been here all day?"

Nate nodded and said nothing.

"I'm sorry for being annoying earlier. I'm just having a hard time with everything." She sat down next to him on the couch. "At least say something."

He grunted and looked at her.

"Why don't you ever tell me what's going on? I mean if you talked to someone, it really wouldn't be so hard on you."

Alex sighed. "I hate being a burden."

"I could never consider you a burden!"

Alex blushed at his comment. She didn't know why she was so happy to know that's how he truly felt.

"Forgive me?" She reached out her hand.

"Forgiven." He shook it.

The rest of the evening was peaceful. Later that night as Alex settled into her bed, she couldn't help but feel that tonight would be different. Maybe she would finally get passed the bright light scene. With this in mind, she closed her eyes and quickly dozed off.

_"…..And then a bright light._"

Alex's eyes opened. She sighed. There really was no getting passed that scene. But she couldn't avoid the dream. She rolled over onto her back and stared at the ceiling. "Why me?" she thought. Then suddenly an invisible force covered her muzzle. Something that felt to her like a handkerchief covered her nose and mouth. She tried to struggle but it was no use. The room around her turned into a blur and then black.

Nate awoke to the sounds of the struggle. He sat up and looked around soon realizing that it came from Alex's room. On the other side of the wall however the invisible creature revealed itself. The chameleon pulled a warp ring off of his wrist and opened a portal. With Alex in his arms, he stepped through it. Nate rushed out of his room. He swung open Alex's door in time enough to see the portal close.

"Alex?!"


	6. Chapter 4

**Chapter 4**

"I can't find any trace of her."

Tails frantically tried to pick up a signal from Alex's chip but it was no use. Each Freedom Fighter had been implanted with a tracker chip just in case something like this would happen. Nate paced up and down Tails' lab while Sonic tried to calm him down.

"Come on man, you need to settle down. When have never been there for our friends? We'll find her."

This didn't change Nate's mood. He was angry at himself for not getting up sooner. He had thought that Alex was rolling over in her bed. She was one to toss and turn a lot during the night because of her dreams.

"Anything yet Tails?", Sonic asked since trying to calm down Nate wasn't working.

"I have a very faint signal."

All three of them gathered around the screen. The signal quickly faded.

"Dang it!", Nate yelled as he stormed out the lab. Sonic went to follow him, but Tails said he should be left alone.

"Did you find anything yet?" Sally asked as she saw Nate leave the lab.

"Nothing at all." Nate dropped his head. "I couldn't save her."

"Hey, don't start blaming yourself. It wasn't your fault." Sally rested a hand on his shoulder and tried to comfort him. "I don't know how many times we've had to save me."

Nate smirked. He thought about all the times that Sonic and Sally would go alone to complete a mission and later on Sonic would return alone. "I let them get her again", he would always say angrily. But it never lasted too long because when the Freedom Fighters worked together they would successfully defeat the villain and save Sally once again.

"Hey Nate", Tails called out as he and Sonic ran out of the lab, "Maybe we should check Alex's room. There has to be some traces left in there."

"Ok then." Nate thanked Sally and then the three went on their way.

_Somewhere in total darkness…_

Alex slowly opened her eyes.

"Where am I?"

She couldn't see anything. She tried to remember what happened but she couldn't get past the splitting headache she had. She rubbed her head and tried to sit up. Her eyes had adjusted to the darkness but there was still nothing to be seen. She shivered as she felt a draft.

"Wait, if I can feel a draft in here then there has to be an opening somewhere", she thought. She began to feel around. After crawling for a bit, her hand came in contact with the wall. She slowly stood up and tried to regain her balance. At that moment the door swung open and a bright light shown through. Alex rubbed her eyes but saw nothing in front of her.

"Hello?"

"I said if you came peacefully I wouldn't have to hurt you." The chameleon revealed itself, his arms crossed in front of his chest.

"What do you want with me?"

"That's for the master to decide. Apparently you are very valuable."

The chameleon stepped inside. Alex backed away from him.

"Don't start this now. I don't want to have to fight you", the chameleon said frustrated.

"I won't go down without one so bring it."

He sighed and shook his head. He then reached into his pocket and pulled out a small leather pouch. He put his hand into it and drew out what looked like sand.

"What is that?"

He blew it into Alex's face and she feel to the floor, sound asleep.

_Back at apartment 207…_

"This is unbelievable", Tails walked around Alex's room with his scanner. "Whoever did this was definitely a professional."

Nate groaned. "I can't think of anything that has happened recently that could be related to this, unless she wasn't telling me something."

Sonic and Tails stayed quiet and looked at each other.

"Don't worry", Sonic padded Nate's back, "She'll be back in no time. We will definitely find her."


	7. Chapter 5

**Chapter 5**

Alex slowly opened her eyes. The bright light caused her eyes to water a bit and her vision was still somewhat blurry. Finally her sight had cleared enough that she could see her surroundings. She tried to sit up but her arms and feet had been cuffed to the table that she was laying on. She lifted her head and looked around. Test tubes and syringes stood on a table next to her.

"This looks nothing like Tails' lab, that's for sure", she said to herself.

"Ah! I see you are awake. Did you sleep well?"

Alex turned her head to catch a view of the speaker. His shadow grew as he stepped out of the darkness. He was a tall, slender man with jet black hair. He wore a long white lab coat with a name tag that Alex couldn't see well enough to read.

"Let me introduce myself. My name is Dr. Argon. I am an expert in the field of Chaos Energy, and you my dear are the missing link to my latest project."

Alex smirked. "You sure you have the right person? I can't manipulate Chaos Energy. You're probably looking for Sonic, Knuckles, or Shadow."

The Doctor raised his eyebrow. "I see. Well I guess we'll just have to run some tests on you to see if you actually are the one I'm looking for."

_...back at New Mobotropolis_

"Thanks for letting me stay here at the headquarters, Sally." Nate was carrying a duffle bag containing all the things he would need during his stay.

"Oh, it's fine. I mean it's not like you've never been here before. Plus I think Sonic will like the male company since Tails' is also locked up in his lab."

Nate had decided to stay at the Freedom Fighters Headquarters while the search for Alex continued. He was lonely in the apartment, and grew angry whenever he walked passed Alex's room.

"Hey man!", Sonic zoomed into Nate's bedroom and stretched out on the bed. "Did you get settled in yet?"

"Yeah", Nate said annoyed, "And I was kind of planning on taking a nap."

"A nap?!", Sonic jumped off the bed, "But I thought you came here to get your mind off of Alex, not to sleep."

"I don't think I'll be able to stop worrying about her." Nate sat down on the bed.

Sonic sighed. "Hey, have a little faith. When have we ever lost? Never! And we don't plan to ever lose. Believe me when I say that we will find her."

Nate nodded. "Thanks bro."

"No problem." Sonic winked and gave him a thumbs up.

"Hey guys!", Tails ran into the room "I think I found something!"

The three of them ran to Tails' lab and planted themselves in front of the large computer monitor.

"It's a faint signal, but I'm picking up a small sense of Chaos Energy on the outskirts of town."

"Chaos Energy? But what would that have to do with Alex?"

"I'm not exactly sure yet, but this Chaos Energy is different than the others." Tails tried to zoom in on the image.

"Different?", Sonic turned to look at Tails, "I thought we all shared the same Chaos Energy."

"We do, but…" Tails got up and walked over to a safe. He unlocked it with a code and pulled out a cyan colored Chaos Emerald. "The Chaos Energy I'm picking up is tainted. It's not pure like the one you and Knuckles manipulate."

"So what does that mean? Does that mean Shadow is involved? Or is someone using the Chaos Energy for the wrong reasons?"

"This is not Shadow's energy", Tails said as he walked over to a machine and place the emerald inside. He typed something into the small screen and the machine started up. Tails stood back and all three of them watched as the emerald began to fade in color. A black aura began to surround it as the color of the emerald turned black. "It's just as I thought."

"What?", Sonic and Nate quickly walked over to look at the screen with Tails.

"Whoever is using that Chaos Energy has tainted it and artificially produced more of it. This many sound odd but I believe that whoever is creating this dark energy has a connection in Alex's disappearance."

"What makes you think that?" Nate grew more concerned now that the issue of dark Chaos Energy was now a factor in the mystery.

"At the time I discovered this energy, you came to us and reported that Alex had been kidnapped. It's just too much of a coincidence."

"Ok", Sonic nodded, "We'll check this place out then."

"I'll use this energy to track its location." Tails began to type codes into his computer.

"See", Sonic turned to Nate, "I told you we would win."

"But we haven't won yet."

"Don't worry, we most definitely will."


	8. Chapter 6

**Chapter 6**

"Prepare the laser."

"Yes master." The chameleon that had captured Alex was now pushing buttons and pulling levers that caused a huge laser gun to light up. A bright yellow aura began to surround the laser as it charged up with Chaos Energy.

"What is that thing?!", Alex cried as she squinted her eyes from the bright light. Her question went unanswered. Instead the table that she was laying on was flipped upwards so that she faced the laser.

"Ready sir", the chameleon held onto a lever.

"Go."

A blast of Chaos Energy shot out and hit Alex right in the chest.

"Ahhhhhhhhhhhhh!" She cried out. The pain was numbing, but after a few seconds Alex could feel her body again, and it felt stronger than ever. She balled up her fists and broke the cuffs around her wrists and kicked out of the cuffs around her ankles. She looked down at her hands. Her fur had changed to a lighter shade of green, and the ribbon that had once held her hair in a ponytail had snapped. Her hair, however, didn't fall onto her shoulders, but instead defied gravity and floated above her head.

"It seems that my calculations were correct. Welcome to the Chaos family Alex, or should a say, Absolute Alex."

Alex was shocked as she caught a view of herself in a mirror. Her eyes were red, her hair was electric blue, and she was emanating a yellow aura. She remembered what Sonic and Shadow looked like in their super forms. She looked no different. "Am I just like them?"

"You are, and maybe even stronger. Work with me and we'll build up your power."

Alex had worked with the Freedom Fighters long enough to know that when someone offered to help with anything involving Chaos Energy the outcome was never good. In the end they would always turn against the FF and try to use the Chaos Energy for their own will which was usually to take over Mobius.

"I would never trust you to help me!" Alex lifted her hand and power began to collect in her palm.

"Oh, no you don't!" The Doctor snapped and ran to the machine where he pulled the lever down. The machine began the suck the energy back. Alex grew weaker by the second as she returned to her normal state. She sank to the ground, unconscious.

"I'll have you working for me whether you like it or not."

_...over in New Mobotropolis_

Tails typed away on his computer. Everyone else had gone to bed but he wanted to stay up and test some things out. All of a sudden one of his energy sensors went off.

"What the…" He jumped off his seat to go check. After pressing a few buttons, the screen showed a variety of bright colors representing the radiation of Chaos Energy.

"That's pure energy", Tails said wide eyed, "the same as Sonic's and Shadow's." Tails tried to track the source but it was being blocked off. "Whoever is using that Chaos Energy is using a force field to mask their location. I have to find a way to penetrate through it."

_…elsewhere in the headquarters_

Nate tossed and turned. He couldn't sleep with Alex on his mind. Finally he gave in and got up. He left his room and went outside. He walked down a pathway into the forest and came across the lake. He sat down by a tree and looked up at the stars.

"Alex, what are you doing right now?" He closed eyes and tried to hear even the faintest sound of her voice, but the night was dead silent.


	9. Chapter 7

**Chapter 7**

"I really need to stop blacking out." Alex sat up and found herself back in the cell she was in before.

"What just happened?" She replayed everything in her head. First there was the laser, and the Chaos Energy, and then…..She shook her head. There was no way that was her. She had to have been seeing things. But she couldn't deny the power that she felt after the energy hit her. She had to face the truth. She was one of them. One of the Supers.

"What did he call me?", Alex thought to herself, "Absolute Alex?" Was that what her super form was called? Alex sat back and thought. More and more questions piled up in her head. Was I born with this power? Were my parents Supers? Does this have any connection to my dream? Alex covered her face with her hands and tried to think of answers for them all. Nothing came to her. This confusion annoyed her but she soon came to see what the real problem was. What was the Doctor planning to do with her?

_...back in Tails' lab_

"Hey guy! I got in!" Tails, Sonic, Nate, and Sally huddled in front of the computer. They watched as Tails' pushed a button which caused a foggy image to turn crystal clear.

"If my calculations are correct, then this is the location of the Chaos Energy source."

"Then what are we waiting for?", Sonic was ready to zoom right out of there, but Sally grabbed one of his quills before he could get anywhere.

"Not so fast. We might know where to go but we still need a plan. We don't know who this person is or what they are capable of. And if he does have Alex, our first mission is to save her."

Nate nodded. "I hope we have the right place."

They spent a few minutes drawing up a plan from the map of the compound that Tails had unlocked. "Ok I think we are ready."

"So who's coming?"

"All of us of course!", Sonic looked around, "I think if it's just us we'll be able to get in and out quickly."

"NICOLE are you coming?" It seemed as if Sally was talking to the air.

"I'll download myself to the portable communicator", a voice replied.

"While you're at it, can you inform the other Freedom Fighters about our mission just in case we need backup?"

"Will do", NICOLE replied. Sally waited for NICOLE to finish as the others looked over the plans one more time.

"Ready?" Sally waved the communicator in her hand signaling the guys to hurry.

"We are coming to get you Alex", Nate said to himself as they walked out the door.


	10. Chapter 8

"How many tests do you plan to run on me?"Alex was annoyed by the fact that she was awakened from her slumber and once again cuffed to the table.

"Until I get what I want", the Doctor replied as he typed on his computer. Alex watched as a chart of her body appeared on the screen. There were two images: one that showed her normal state and one that displayed her super form. Codes and other charts filled the screen around her image.

"Chase!"

The chameleon came out of his camouflage form. "Yes master?"

"Here." The doctor handed the chameleon a syringe needle. "Make sure all of it is used."

"Yes sir." The chameleon camouflaged and made his way towards Alex. She didn't notice until she felt a sharp pain in her arm.

"Hey! What are you…" Her mouth closed. Her mind went blank and her body froze.

"Alex?", the Doctor snapped his fingers. The cuffs around her wrists and ankles unlocked and she stood up. Her eyes were blank, as if she was being possessed.

"Yes master." She bowed in front of him and waited for an order. She was now under his control.

_….on the outskirts of Mobotropolis_

"Where are we?", Sonic asked looking around.

The Freedom Fighters made there through what seemed like ruins left from the old Robotropolis. Tails' led the group, holding a GPS in his hand pointing it at different rundown buildings to see if they had reached their destination.

"I thought we had cleaned all this up after New Mobotropolis was built", Nate said.

"I guess we missed a few spots", Sally replied. They kept walked until Tails' GPS began to beep. They all stood in front of an abandoned factory.

"I guess this is the place." Tails turned off the sound on his GPS. "Do you hear anything Nate?"

Nate closed his eyes and listened carefully. He could hear the beeping of machines and someone typing on a computer. And then it hit him.

_"…Yes Master.."_

He knew that voice anywhere. It was a voice he missed hearing. It was Alex. He quickly opened his eyes.

"She's in there!" Nate wanted to rush in but Sonic held him back.

"Slow down there. We can't just barge right in there. That would be rude", Sonic smirked.

They quietly opened the door and slipped in.

"I can sense a security system in here", NICOLE said, "I'll tap into it and shut it down."

Within seconds the lasers and motion sensors shutdown due to NICOLE's tap into the system. The gang made their way through the maze of the factory that was displayed on Tails' GPS.

"It says there is an underground compound here." Tails stopped in front of a stairwell that went down. It was dark and musty, as if it hadn't been used in awhile.

"So who's first?" Sonic turned to look at everyone.

"I'll go." Nate led the group quietly down the steps. It seemed as if it was never ending as it spiraled downwards.

"Jeez, how deep are we?" Sonic asked stopping to take a break after walking down the flight of stairs.

"About 20ft. underground", Tails replied. They walked down a corridor until they reached a door.

"Great, another door. Is there going to be stairs behind this one too?" Sonic impatiently waited as Tails unlocked it. He slowly pushed it open. Just as they stepped in an alarm went off.

"NICOLE, I thought you shutdown the system!", Sally yelled over the loud beeping of the alarm.

"I did. There must have been a backup that I didn't sense!", NICOLE replied.

_….in the lab_

"We have intruders! Chase, go see what the problem is."

"Yes master." The Chameleon disappeared. The doctor turned to his computer and changed the screen to view a camera.

"Ah, are these your friends?" The doctor watched as Tails, Sonic, Nate, and Sally ran through the hallway. "Should we give them a nice welcome?"

Alex said nothing. She just stood her post waiting for the Doctor to tell her what to do.

"Alex, why don't you greet them for me?"

"Yes master." Alex turned and ran out of the lab. The Doctor snickered and looked back at the screen, waiting for the show to begin.


	11. Chapter 9

"This is endless!" Sally and the guys ran through the hallway, but it never seemed to end.

"You are not welcome here." Chase revealed himself to the Freedom Fighters.

"Are you the one in charge here?", Sonic asked stepping in front of Sally.

The chameleon ignored his question and lunged at Sonic.

"I guess we'll never know", Sonic said holding him back. They fought, swing fists and feet at each other. The other Freedom Fighters tried to separate them but whenever they got close Chase would camouflage.

"It's no use!", Sonic yelled at them, "Go on ahead and find Alex! I'll keep him busy!"

The Freedom Fighters turned to go but were stopped by a familiar voice.

"Looking for me?" Alex stepped out of the shadows and into view.

"Alex!" Nate ran towards her and through his arms around her. "Thank goodness you're OK!"

"Who are you?"

Nate's heart sank. "It's me. Nate."

Alex did not reply. She stared blanking at him.

"Alex! It's me!" He shook her but got no response. He looked into her eyes. Their usual purple color was no longer there. He had never seen such blank eyes.

"This isn't Alex. They did something to her!" He turned to look back at Tails and Sally.

"Nate! Watch out!" Nate responded too slowly. Alex's fist hit him square in the muzzle. She broke herself from him grip and began to prepare to fight him.

"Alex, what are you doing?" Nate ducked from her punches but refused to hit her. Finally, he threw himself at her and pinned her down.

"What's wrong with you?!"

Alex ignored his question and stayed silent. This wasn't the Alex he knew.

"Well I guess you didn't enjoy your welcome." Another figure stepped out for the darkness. The Freedom Fighters stoop up and looked at him. "My name is Doctor Argon and welcome to my lab."

Alex pushed herself free from Nate's grip and stood up. She walked over to Chase and helped him up, and then took her place next to the Doctor.

"Who are you, and what have you done with Alex?"

The Doctor laughed. "I helped your friend. I didn't harm her."


	12. Chapter 10

_…in the lab_

Alex trailed behind the doctor as he took them through the lab. Nate tried to stay close behind but Chase blocked his path. Nate concealed his anger and stayed back with the rest of the group.

"How about we give your friends a demonstration, Alex?" The doctor prepared the laser gun.

"Yes sir." She stepped in front of the gun, and waited.

"Alex! Watch out!" Nate ran to jump in front of the machine but Sonic held him back.

"Nate! That's Chaos Energy! Watch it!"

Nate looked up just in time to see the energy hit Alex. He watched in horror as she cried in pain. Alex took it all in and the Doctor turned off the machine. She fell to her knees.

"Alex!" Nate jumped up and ran over to help her up. She pushed him away. The force was so strong that he went flying into one of the lab benches.

"Nate!" The Freedom Fighters ran to his aid and then turned to look at Alex. She slowly stood up, her body glowed and her hair floated. Her eyes were a deep red. She lifted her head and looked up at them.

"Don't you see", the doctor said, "I helped your friend discover her true power."

Sally and Tails helped Nate up as Sonic walked over to Alex. "Is she…?"

"Manipulating Chaos Energy?", the doctor finished his question. "Thought you and Shadow were the only ones that could?"

Sonic couldn't believe it. "Alex, say something. Are you in there? Is this really you?"

She did not answer. She stood as still as a statue. She had no control of her body or mind.

"Well now that you know, I think you should leave us be." The doctor turned his back to them. "Alex, dispose of them."

Alex bowed her head and turned to the Freedom Fighters. "Leave peacefully and I won't use force."

"Peacefully?", Sonic smirked, "I don't do peacefully, especially when a friend is in danger."

"As you wish." Alex lifted her hand and Chaos Energy began to collect. Sonic dodged the blast. He ran in circles around her, hoping to cut off her air supply. She flew out of his vortex and stopped him with another blast from her hand. She used the energy to grab him and hold him. With her other hand she grabbed Sally, Tails, and Nate.

"Alex, don't do this! We're your friends!"

Alex ignored them as Chase opened a portal with a warp ring. She moved them to towards the portal just as Nate gained some consciousness.

"Alex…wait…"

She threw them through the portal and sealed it.

_…at the wasteland of old Knothole Village_

A portal opened and threw out Sonic, Tails, Sally, and Nate before closing.

"Wow", Sonic adjusted his quills, "He wasn't kidding when he said dispose of us. He took us out like we were trash."

"This isn't time for jokes Sonic", Tails beat the dirt from between his tails, "We have a HUGE problem."

All four of them made their way to New Mobotropolis. It was a long walk through the forest to get back. Sonic, Tails, and Sally walked and talked about recent events while Nate walked behind. He didn't think it would get this bad. He had hoped that all they had to do was waltz in there, save Alex, and beat the doctor. But instead he discovered Alex's true capabilities, and that she had no idea who he was.

"Hey? Are you ok?" Sally had noticed Nate's absence from the conversation and stayed back to walk with him.

"I don't know", he replied, "How did all this happen? Why didn't she tell me about her powers?"

"She couldn't have known", Sally sighed, "The doctor told us that he helped her discover them."

"What we going to do?"

"I don't know yet", Sally looked up at the sun through the trees, "But we will come up with something to save her."

_…back at New Mobotropolis_

"She's what!?"Amy gasped at the news.

A meeting of the Freedom Fighters had been called into session. Attendees included: Sonic, Sally, Amy, Mina, Tails, Bunnie, Antoine, Nate, and NICOLE.

"She's a Super. She can use Chaos Emeralds just like Sonic and Shadow", Tails repeated to the entire group. Tails went on to tell everyone what had happened in the abandoned factory. "Whatever that Doctor is planning can't be good. I sensed the presence of tainted Chaos Energy from his lab one night. He is somehow mass producing it. If he was to use it on Alex it could be fatal. He has her under his control in some way, and with her powers he could cause some serious damage. We need to come up with a plan to not only save Alex but to also destroy the Doctor's Dark Chaos Energy."

_…in Doctor Argon's lab_

"Ok Alex one more test for today." The Doctor inserted a black Chaos Emerald into his machine. He aimed the laser gun at Alex. After pressing a few buttons he counted to 3 and then pulled the lever. A wave of dark energy flowed through the machine and out the gun. It hit Alex, but the effects were different. She still cried out in pain but that eventually pasted. Her fur and hair turned to a darker shade and her clothes turned black. The Doctor turned off the machine and marveled at his attempt. Alex slowly lifted her head and opened her eyes. Her iris and pupils had disappeared which left her eyes glowing white.

"I like this form a lot better", the Doctor laughed.


	13. Chapter 11

Days passed and plans were made on both sides of the conflict. The Freedom Fighters had alerted all their counterparts in other areas. They worked meticulously on a plan that would help them to execute a successful rescue of Alex and demise of the Doctor. On the other hand, the Doctor had plans of his own. He found ways to use the Dark Energy to its fullest, and Alex, the center of his operation, was slowly falling deeper into his grasp. She was no longer a mindless zombie but she still followed under his command, and day by day her body grew weak from the intense radiation of Dark Energy that was used on her.

_…in New Mobotropolis_

Nate left Tails' lab and headed down to the HQ. It had been about a week since he had last seen Alex, and he impatiently awaited the next time, which he was sure would be the day that they would liberate her from the Doctor's hold.

Tails and Sally stayed behind to go over their plans one last time.

"OK?", Sally said looking at the computer screen. She had video called Knuckles and the rest of Team Chaotix to fill them in with the details.

"OK Sally", Knuckles replied, "I think we have it. We will stand our posts until we get your signal."

"Good." Sally connected NICOLE to the computer to transfer information. "We need to be prepared. We don't know when the Doctor will strike, but when he does we need to be ready for him."

"Right." Knuckles nodded and then said his goodbyes.

"Tails", Sally turned to address the two-tailed fox, "do you think we can match this guy? I mean, he does have his own Chaos Emeralds, and they're tainted. Plus, he has Alex, who would be able to use their power."

Tails fussed with one of his machines and then stood up. "Of course we can. We have Sonic and Knuckles who can also use Chaos Energy. Plus we have the whole team. We'll be fine. Also, even though Alex is under the Doctor's control, there could possibly be a way get through to her. She couldn't have just forgotten all of us like that. I have a feeling that the Doctor's mind control is actually a memory block."

"So if we could just tap into her memories", Sally suggested, "We could get her back on our side and defeat the Doctor."

"Exactly", Tails nodded, "And I have a feeling that Nate is the perfect person for the job."

_...in Doctor Argon's lab_

"OK, that's enough for today."

Doctor Argon signaled for Chase to turn off the machine. It sucked back all the Dark Chaos Energy it had released, and stored it in the Black Emerald. Alex, now back in her normal form, fell to her knees, weak from the impact the energy was having on her body. Chase, who had now somewhat become fond of Alex's company, went to help her up. The Doctor shoo-ed them away as he went back to his studies and they both left the lab.

"How are you holding up?", Chase asked as they made their way through the corridor.

"It hurts", Alex replied, holding her arm, "But let the master's will be done. He said it would make me stronger if I got used to it."

Chase sighed. "You're lucky you know."

"How so?"

"The doctor sees you as his prized possession. You have a lot of power and potential", Chase begun. "He used to run tests on me as well. The outcome wasn't as great though. He thought he could become the next Professor Gerald Robotnik, and create another Ultimate Life Form. I was his first test subject."

"…Robotnik…", Alex mumbled. That name sounded so familiar but she couldn't remember why.

They reached the exit to the factory and walked outside. During the times that the Doctor wasn't running tests on her, Alex hung out with Chase outside the factory. There had been a boundary set by the Doctor so they couldn't go too far. Alex sat in her usual spot, the top of an old trash bin, while Chase picked up a rock and through it against the brick wall.

"Who is Gerald Robotnik?", Alex asked looking up at the clouds.

"Not exactly sure", Chase went to pick up the rock that he had thrown, "Doctor Argon is always talking about him. The guy is like his idol or something. Have you ever heard stories of the Ultimate Life Form?"

Alex thought for a second. _The Ultimate Life Form._ Why did that ring a bell in her head? She leaned back against the brick wall and closed her eyes. She thought back. Way back. Everything was a blur.

"It sounds familiar, but I don't remember what it is."

"Oh", Chase threw the rock again, "He was creature created by Gerald Robotnik. He's apparently immortal and can also manipulate the power of Chaos Emeralds like you can."

"So is that why the Doctor is always running tests on me? So I can become an Ultimate Life Form?"

"I think so, but the thing is, you're not immortal."

After Chase said that, Alex watched her life flash before her eyes. If the Doctor's experiments failed would she die? She shook the thought out of her head.

"Looks like I have to get stronger so my mortality doesn't matter then."

Chase nodded. At that moment, they both felt a shock through their bodies. The doctor was calling them.

"Back to work."

They both made their way towards the entrance of the factory.


	14. Chapter 12

"Yo, bro."

Nate looked up at Sonic, who was standing over him.

"What's up?"

"Just thinking." Nate pulled his knees in tighter, as Sonic sat down next to him.

"You really miss her, don't you?"

Nate sighed. "Yeah. It's kinda weird not having her around."

"Ha yeah", Sonic smirked as he lay back in the grass and closed his eyes, "Kinda quiet. A little too quiet for me though."

Nate let go of his knees and leaned back, looking up at the sky. "How long do you think it's going to take the Doctor to strike?"

Sonic shugged. "Who knows. Tell you the truth I'm getting kind of impatient. I mean, I'M WAAAIIIITTIINNNGG!"

Nate laughed. Sonic really knew how to make someone feel better with his witty ways and silly expressions. The two sat quietly for a few minutes. Then Nate spoke up again.

"Do you think she'll remember me when we save her?"

Sonic smirked again. "What damsel in distress forgets her knight in shining armor?"

Nate blushed at the comment and turned to conceal his face. Sonic opened one eye and took a peek at him. He reclosed his eye and smiled a bit. _"Ha ha, I hit a soft spot."_

_…at Doctor Argon's lab_

"Alex", the Doctor handed her a pair of golden cuffs, "Put these on."

Alex looked down at the golden bracelets and then slid them onto her wrists. They seemed kind of heavy at first but she gradually grew accustom to them.

"Ok, now let's test them out."

The Black Emerald was inserted, the machine was turned on, and she stood at her post, closing her eyes as she waited to be blasted by the energy. It hit her, and the usual pain came with it, but within a few seconds she felt the power surge throughout her body. The Doctor snapped and Chase turned off the machine. Alex stood up straight and opened her empty eyes. She balled up her fists and waited for a command.

"Power down." The Doctor pointed a remote towards Alex. The cuffs seemed to suck all the Dark Energy and once again Alex was in her normal state. She didn't feel as weak as she usually did when the energy was sucked out of her. She looked down at the bracelets in awe.

"Power up." The Doctor pressed the button again and the energy was once again released. Within a few seconds the energy traveled through her arms to her entire body. The doctor nodded with content. "Now I have total control."

After a few more test runs the results were clear. The Doctor no longer had to the shoot Alex with the Dark Energy he stored in the emerald. The energy was now stored in the power rings that Alex wore on her wrists. With the simple push of a button she could transform from Alex to Dark Absolute Alex. The rings also restricted the energy, keeping it from going out of control.

"The time has finally come!" The Doctor laughed madly. "With this, I'm unstoppable!"

Back at his lab, Tails' Chaos Energy sensors rang off the hook. All Freedom Fighters gathered in the lab to watch as Tails displayed the source.

"It's time."

Sally quickly instructed NICOLE to shield off the city. She then got through to Knuckles and Team Chaotix warning them to be ready. After that, with everything in check, the Freedom Fighters took off.

The fight was about to begin.


	15. Chapter 13

"Let's go."

The memory block that the Doctor had injected Alex with a few weeks ago had begun to wear off so she was given more. All her memories that did not include the Doctor or Chase were once again wiped clean from her mind.

Chase was fussing with the Chaos generator, preparing it for its last use. It had been decided that all the dark energy would be stored in Alex's power rings, since it would be the only thing needed by the Doctor to achieve his goal of world domination. Alex stood and waiting in front of the gun. The Doctor pushed the button on the remote and Alex transformed. Chase then fired the dark energy at her. She grit her teeth, and tightened her arms around her chest. The power was great, yet she felt as if it was too much for her to handle. Chase and the Doctor stood clear of the machine, knowing that leaving it on would cause it to explode. The emerald within the machine had reached its limit, and cracked a little, causing a huge blast. Within a few seconds the entire factory had been destroyed. The Doctor peeked out from his hiding spot. The smoke and flying debris blocked his vision, but soon an unharmed Alex came into view. She was surrounded by a black aura, more intense than that of the one she had when only hit with a little dark energy.

"Alex", he called to her. She answered him by stand up from one knee, lifting her head, and opening her bright empty eyes.

"You know what to do."

She nodded, and she was off.

_…on the outskirts of Mobotropolis_

"Ok. Everyone knows their post?"

The eight Freedom Fighters nodded their heads and left for their positions around the city. Nate had a position in the Great Forest, but before he could leave Tails held him back.

"Hey Nate, there is something you should know about Alex's condition."

Nate's heart skipped a beat as he thought about all the horrible things that Alex could have went through. "Yeah, what about it?"

"Well I think that the Doctor blocked Alex's memories instead of erasing them. The way she responded to us last time made it seem like we were still familiar to her." Tails' Chaos Sensor began to beep even louder.

"Blocking them?", Nate spoke over the sound, "How do we unblock them?"

"Not sure", Tails said as he took flight, "But you might be the one that can tap into them." With that Tails took off to get into his position.

_"Me…? Why me?"_

Nate headed towards the Great Forest. With his echolocation abilities he could hear noises from deep within it. He walked slowly, turning to look in every direction he heard a sound. The leaves and branches of the trees above him shook in the wind that passed. He looked up at the rays of sunlight that bled through the gaps between the leaves. And then everything went still. He stood still, his ears perking up, catching any sounds they could. He closed his eyes so he could focus more.

"Looking for me?"

Nate opened his eyes and looked around. Nothing stood in front or behind him. He looked left and right but nothing was to be seen there either. Then he looked up. He caught view of a dark creature, cloaked in a black aura. It leaned against the bark of the tree as it sat on a branch above Nate's head.

"It's not safe to be in the Great Forest alone." The creature smirked, turned in his direction and opened its eyes. Nate shuddered to see that they were blank and glowed intensely as if they could see right through him. He stood there and stared back at the creature not saying a word.

"You really know how to greet someone." The creature stood up and hopped of the branch. It steadied itself in front of Nate and then stood up.

"A-Alex..?" Through all the darkness he could see her. Her hair flew above her head and eyes stayed fixated on him.

"Alex what happened to you? This isn't you."

"What would you know", she smirked, "You don't know me."

Nate stepped a little closer. "Yes I do, and this isn't the real you."

Tapping into her memories wasn't going to be an easy task. Alex in this form was even more stubborn than she normally was and it was going to be difficult to get past the Dark Energy that she could blast him with at any moment.

"So where is the rest of your crew?" Alex crossed her arms in front of her chest impatiently.

"You don't need to know."

"Oh?", Alex laughed a little, "So it's going to be one on one then?"

"I'm not going to fight you."

"Afraid to hit a girl huh?" The energy began to collect in the palm of her hand. "Well that makes my job a lot easier."

She aimed her hand at him, and like a whip, a string of Dark Chaos Energy shot out and wrapped around his neck. She closed her hand into a fist, which tightened the hold. Nate struggled to break free but he could not grab at the band of energy around his neck.

"This is too easy." She laughed at him as he wriggled in her grip. Then, like she was about to throw a ball, she swung her arm back and then threw it forward, releasing him by opening her palm. Nate went flying, skidding the ground for a bit before coming to a complete stop. He coughed a little as he lay there and he was too weak to respond to her attack.

"One Freedom Fighter down", she dusted her hands and turned her back on him, "7 more and a whole city to go."

The dark aura surrounded her once more, and she vanished.


	16. Chapter 14

**Chapter 14**

She could sense her next targets as she traveled among the trees. She came upon another clearing in the forest, this one being occupied by two female Mobians.

Amy and Mina stood back to back so they could survey in all four directions.

"Did you hear that?" Amy lifted her hammer and looked around.

"It was just the wind passing through." Mina crossed her arms to her chest. They stood there in silence for a few more seconds. Then, all of a sudden, they were surrounded by a black fog, which masked their vision.

"Whose there!?" Amy yelled, lifting her hammer, blindly swinging it around. Mina tired to find her way out, but moved too far from Amy. Alex had accomplished her goal of separating them. Now she could take them down one by one.

"Boo." Amy stumbled back a little at the sight of Alex's eyes glowing through the fog.

"Stay back!" Amy swung her hammer at Alex, but Alex was quick and jumped over it.

"You think you can stop me with a hammer?" Alex snickered.

"Alex?", Amy said, recognizing the voice.

"The one and only." Alex stood in front of her, hands on her hips. She lifted her palm and the dark energy left it and grabbed Amy, taking a firm grip around her waist. Alex hoisted her up in the air.

"Alex! Don't do this!", Amy screamed, swinging her hammer at the band of energy that held her.

"I'm only doing what I was ordered to do." Alex left Amy and began her search for Mina.

Mina however was making use of the time she had before she was captured. Through a watch that Tails had given her she had communicated the rest of the Freedom Fighters and sent her coordinates to them. They replied saying that would be there right away.

"There you are."

Like the tentacles of an octopus, the Dark Energy that Alex shot at Mina grabbed her and lifted her up.

"Mina!" Amy shouted as she saw Mina being held by her wrists. "Hold on!"

"I reached the others and they are on their way!" Mina yelled back to her.

"More people for me to capture? Sounds like fun." Alex hovered at their height and leaned back against a cloud that had been formed from the darkness. "I guess I'll just wait then."

Alex didn't let go of Amy or Mina as she waited. Mina's arms were slowly going numb from being held up for so long and Amy had grown tired of swinging her hammer around.

"Alex!"

Alex's eyes met Sonic's as he and the other Freedom Fighters arrived at the scene.

"For the fastest thing alive, you're pretty slow." Alex smirked. She lowered herself and stood before them.

"Alex! Let them go!", Sally stepped up next to Sonic, "We are not your enemy!"

"I have come to claim what rightfully belongs to Doctor Argon. That means I must dispose of those who stand in his way. If you stand in his way, you are his enemy, therefore making you mine as well."

"Jeez, he totally brainwashed you."

Alex ignored Sonic's comment and went on. "So who will challenge me first?"

No one moved. They weren't exactly frightened but they couldn't predict Alex's moves.

"No one?", Alex shrugged, "I guess I'll just have to take all of you out like I did that pathetic hedgehog earlier."

"…hedgehog..?"

Sally gasped at the comment and turned to Tails. "She's talking about Nate! We need to find him and make sure he's ok. We need him, in order to save her."

"Tracking him now." Tails began to type on his communicator.

While Sally and Tails were busy trying to locate Nate, Sonic, Bunnie, and Antoine dealt with the issue at hand.

"I'll give you a challenge", Sonic said stepping forward, "Try and catch me."

Alex smirked. "You think I would be stupid enough to waste time and do that?"

"Well if you were so keen on obeying your master, you wouldn't really have a choice."

Sonic curled up into a ball and did a spin dash into the black fog. This was meant to be a distraction while Bunnie and Antoine found a way to free Mina and Amy.

Alex, realizing that Sonic was right, dove into the fog in search of him. After she disappeared Bunnie prepared her laser gun and shot it at the bands of energy holding Amy, and then Mina. The energy faded and both girls were released. Bunnie caught both of them before they hit the ground. They were both sore from hanging so Bunnie put them down and shielded them.

Alex had sensed Bunnie's shots, but ignored them. She knew that if she brought Sonic down she could quickly eliminate the rest of the team. He had become her key target.


	17. Chapter 15

**Chapter 15**

Sonic wandered around aimlessly. He knew that Alex had followed him inside, and was well aware that she could quickly find him no matter where he went. But his goal was to bring her to him. If he could at least get behind her quickly enough he could grab her. The only thing that worried him was the dark energy. He had no idea how it would affect him.

_If I absorb that energy will I become just like Alex?_ He thought as he ran. _Wait, I also have to factor in the part about the Doctor brainwashing her. That's it! It's not the Dark energy doing this to her. It's the Doctor._

Sonic had remembered the time he had become Dark Sonic. It wasn't due to him becoming evil. It was because he had been so irritated by the fact that his friends were hurt that he couldn't hold back his anger. He still had control of his powers and knew his enemies from his friends.

"Where are youuu…?"

He heard her voice in front of him. Being careful not to reveal his hiding place he stopped and stood still. There she was, walking slowly so she could see in all directions. Sonic knew he had to act quickly while her guard was down. He watched as she turned her back to him. All he needed was a second. He jumped and spun himself up into a ball. He sped towards her. By the time Alex heard him it was too late to avoid his attack. He spun into her, knocking her off her feet. She tried to quickly recover, but Sonic grabbed her. He stood behind her and put her arms behind her back.

"Let go of me!" she struggled to free herself from his grip. She grew angry and the dark energy around them intensified.

"If you do that, I'll absorb all your energy."

Alex laughed. "You can't absorb this energy. It's stored in my power rings."

"What?" Sonic looked at her wrists and saw the two gold power rings that she wore. Alex took this opportunity to break from his hold. She jammed her foot into his. He jumped which caused him to let go of her.

"How sad." She pointed in his direction and shot the energy at him.

"Ahhhhh!" The energy engulfed him and slowly brought him to his knees.

"Farewell, Sonic the Hedgehog."

"Sonic! No!"

Just as Alex was about to deliver the final blow, she was knocked to the ground by what seemed like a giant hammer. The impact hurt more than Alex thought it would. Now that she had been weaken the dark fog that surrounded to the clearing in the forest began to fade.

"Don't you dare try and hurt my Sonic!" A recovered Amy posed with her hammer hoisted behind her back.

"Thanks Ames." Amy helped Sonic back to his feet.

Alex slowly stood up. Her power rings began to glow at the sense of a Chaos Emerald nearby. The wind blew harder, and a huge shadow came over them.

"Have you failed me Alex?" A voice came from the ship that hovered over their heads. They all looked up. Sally and Tails had returned with a conscious Nate just in time to see the ship as well.

"I thought you were strong enough to destroy the Freedom Fighters. I guess I was wrong."

The ship landed and the Doctor stepped out, Chase by his side. "So Freedom Fighters, we meet again. I was hoping we wouldn't have to though."

The Freedom Fighters gave no reply.

He turned to Alex. "I was hoping I wouldn't have to do this but you leave me no choice. You need all the power you can get."

He pulling out the remote and pushed a button on it. It unlocked the power rings around her wrists and released all the dark energy.

"Ahhhhhh!"

Alex no longer had something to help her control the energy. She knew she wasn't strong enough to use all of it at once. She fell to knees.

"Wait Doctor, she can't handle all of it at one time!" Chase watched as Alex clenched her fists.

"She'll adjust to it." Doctor turned to her. "Alex take it in! You will never feel power this great again!"

Alex heard his words and obeyed. She ignored the pain it caused and allowed to manifest. Before long, it began to numb her entire body that she could barely feel it.

"That's it!", the Doctor grew ecstatic, "Now destroy the Freedom Fighters! Destroy Mobotropolis!"


	18. Chapter 16

**Chapter 16**

Alex now stood at the entrance of Mobotropolis. She had used her Chaos Control to get a head start and was now trying to find a way to break the force field that protected the city. The energy was slowly taking over her body. She grew weaker every second though she did not notice. The Doctor's memory block caused her to only focus on his wishes, even if it meant she sacrifice herself.

"I guess I'll just have to break through." She lifted her palm and the gust of dark energy left her hand, boring straight into the force field. After a few second the field began to deteriorate.

_...back in the Great Forest_

Sonic sped through the forest with Sally in his arms. They had left the rest of the Freedom Fighters to take care of the Doctor.

"…Sally, she's breaking through the barrier. I'm not sure I can hold her off much longer. Her power is too strong…"

"Just hold on NICOLE. Sonic and I are on our way."

Sonic finally exited the maze of the forest and came upon the entrance to the city, where Alex stood, using her power to penetrate the field.

"You're too late." Alex intensified her last blast and the force field disappeared. Alex shot them an evil grin and cloaked herself in the dark energy. She vanished before their eyes.

"She's in the city! Hurry Sonic!" Sally pointed towards the city and Sonic picked her up again.

_…in the Great Forest_

The goal of the other Freedom Fighters was to get hold of the Doctor's tainted Chaos Emerald. While Bunnie, Antoine, and Nate distracted the Doctor, Tails flew into the ship to survey it. Chase was being held off by Amy and Mina, and although he was able to camouflage he wasn't fast enough to avoid Amy's hammer.

"It has got to be in here somewhere." Tails looked everywhere but couldn't find the emerald. He remembered how Alex's power rings had glowed with the Doctor came, which meant that the emerald had to be nearby. Tails looked at his Chaos Energy sensor. It detected a small amount of energy coming from what looked like a safe. He walked towards and the signal grew stronger.

"Found you." Tails fiddled with the lock until he successfully broke the code. He opened it, and there he saw the black emerald.

"You need to be purified right away." He grabbed it and flew out the ship.

"Hey you guys!", Tails waved his hand, "I have the emerald. Now let's go help Sonic and Sally."

The others nodded. They had already worn out Chase and the Doctor, who both sat breathless against a tree.

_….in Mobotropolis_

Alex stood at the top of the highest tower in the city. She looked down at all the subjects of the city, who were unaware of what was about to be unleashed against them.

"Let the show begin."

She lifted her arms and the dark energy left them. The sky turned black and strong winds blew. Down below the ground began to shake and crack. Mobians stood still in fright, trying to figure out what was going on.

"Sonic!"

Sonic stopped. Sally's cry had made him aware of the situation. People began to run past them, trying to get to away from the destruction.

"NICOLE! Take everyone into the forest and shield them off!"

"Will do Sally." NICOLE's hologram appeared in front of them and then took off to guide the citizens to safety.

"What now?" Sonic looked around trying to find Alex. It had grown too dark, and the source to was hard to location.

"We need to get in touch with Knuckles. From Angel Island he should be able to see what going on from a safe distance."

Sally dialed for Knuckles with her communicator.

"We're here Princess", replied Team Chaotix, as they answered the call.

"Knuckles, can you see what's going on?"

"Yes I can, and I can see Alex as well."

"Do you think you can get a good shot at her?"

"From where she is now, yes, but try to keep her there."

"Ok, we'll be in touch then."

Sally ended the call and looked at Sonic.

"So what do we do now?", Sonic asked as he avoided running Mobians.

"We have to wait. If we distract her, she will definitely move. Our goal to is to use the Master Emerald's power to purify her. If Knuckles doesn't have a shot at her it won't work. We have to be spot on."

"But Sal, it isn't the Dark Energy that's causing her to be this way. It's the Doctor's memory block. We have to break that before we purify her."

"How are we going to do that? Nate's still weak from the previous attack."

"Then it's going to take all of us together to bring her memory back."


	19. Chapter 17

**Chapter 17**

_…the city is crumbling to the ground. People are trying to flee. The world is in complete and total chaos._

Alex sat and watched as the city shook under her. She caught view of the Freedom Fighters, who were busy trying to help people escape. She laughed.

"Run if you can, it won't matter now. Your city now belongs to Dr. Argon."

_…at the entrance of Mobotropolis_

"Hurry everyone!"

Last of Mobotropolis' citizens were making their way out. Finally with the city cleared, the Freedom Fighters could focus on their target without putting anyone in danger.

"Nate! We need to unblock that memory block!"

Nate looked up at all the chaos. _"Why do I feel like I seen this before? This setting is all too familiar."_

"Tails, can you take me up there?"

"Sure but…"

"ARE YOU CRAZY!?", Sonic interrupted Tails, "You could get killed!"

"I have no choice! What affect will I have on her if I stay down here?"

"He's right", Sally sighed worriedly, "We don't have a choice. He has to go."

Nate nodded and grabbed hold of Tails hands. Tails flew up the building from the back so Alex wouldn't notice them.

"Tails go back. We can't risk having you hurt as well."

"But…" Tails frowned as he set him down on the rooftop.

"I'll be OK."

Tails left, and Nate composed himself.

"Alex!"

She straightened her back to her name and turned to him.

"Oh, not you again. Didn't I already take care of you. Are you back for more?"

He ignored her and stepped closer. "Alex listen to me. This isn't you. Dr. Argon isn't your master, he's just using you."

She laughed. "You think I'm going to believe you?"

He ignored her once again and continued. "He's just using your power! Don't you see?!"

She shook her head. "I've heard enough."

She lunged at him, tackling him to the floor. She wrapped her hands around his neck.

"Any last words?", she asked as she began to tighten her grip.

He didn't fight her, but he was able to choke out 4 more words.

"Alex… I…Love…You."

She felt a shock run down her back. "What?"

She looked down to see an unconscious Nate under her.

"Nate?!"


	20. Chapter 18 (End)

**Chapter 18**

"Tails, can you see what going on?"

Tails, flew back to the rooftop to get a better view. There he saw an unconscious Nate, and a worried Alex.

"He did it! She's back to normal!", Tails said into his communicator watch.

"Good! Now make sure she doesn't move."

Sally contacted Knuckles and told him that everything was set. "We're ready Knux!"

"Got'cha", he replied. He got a lock on his target, and began to chant. The Master Emerald, on which he stood, began to glow. He directed its pure energy towards his target.

Alex grew weaker by the second. Now that the memory block was gone, she was fully aware of the power that she was unable to control. She had moved away from Nate, in fear that the dark energy would make his condition worse. She was on her knees, struggling to stay up.

_And then a bright light…_

It hit her square in the back. She cried out in pain as the Master Emeralds' power purified the tainted energy. She fell, and her eyes began to shut. The last thing she saw was a blurry image of Nate's body laying beside her.

_…2 weeks later at TT Memorial Hospital_

_…the city is crumbling to the ground. People are trying to flee. The world is in complete and total chaos. And then a bright light…_

Alex opened her eyes. She sat up and rubbed her head. She looked around and realized she was in the hospital.

"Hey everyone, she's awake!"

Before Alex knew it, she was surrounded by all the Freedom Fighters.

"You put up quite a fight." Sonic crossed his arms in front of his chest. "But we won't blame you for it."

"Thank goodness your ok though", Sally said pushing Sonic aside. "Nate was able to get you back to normal."

Alex looked around. "Where is he?"

"He's getting one last check up", Amy replied.

Alex sighed. "I'm sorry. I didn't mean for all this to happen. This is all my fault."

"Hey", Sally squeezed her hand, "We're just glad your back on our side."

"Ya, and if you want to play the blame game", Sonic added, "We should all point fingers to that doctor dude that started this whole mess."

"Well thanks to him", Tails said, "We discovered Alex's true power."

This was a knock at the door. "How's my patient doing."

Doctor Quack stepped in through the crowd. He was followed by another, a hedgehog, who had a bandage on his and arm and a few bruises here and there.

"Nate, I see your feeling better." Sonic went over to pat him on the back. Nate grimaced at the pain but was able to nod and crack a smile.

Alex couldn't see Nate behind the crowd. She was receiving a check up from Doctor Quack and everyone had started their own conservations.

"Well your good to go as well." Doctor Quack used his stethoscope to check her heartbeat one more time.

The boys were kicked out of the room so Alex could get dressed, and when she was ready, the whole group left the hospital together. Alex and Nate stayed a little behind. They didn't say a word to each other and stared at the ground.

Alex finally broke the silence. "I'm sorry."

"For what?"

Alex rubbed her arm. "I feel like I could have prevented this whole thing if I had just told you what was going on."

"Well what good would that bring? We probably would have never discovered that you could turn super if it wasn't for all of this."

"I'm not sure it was worth hurting you though."

Alex blushed at her reply. Nate turned his head slightly to hide his burning cheeks.

"It's ok. Everything is fine now isn't it."

Alex looked around. The repairs around Mobotropolis had really progressed during the 2 weeks she had been in the hospital. It was starting to look like home again. They continued to walk behind the other Freedom Fighters. The group was planning to have a Welcome Back party at the headquarters.

"By the way", Alex started up again, "What did you say that made me come back?"

Nate's heart skipped a beat. "I don't really remember", he lied.

"Oh." Alex couldn't remember either. "Well maybe you'll have to use it again if I'm ever captured by an evil doctor and put under a memory block", she said laughing.

Nate blushed. "Maybe." He hoped that one day he would have the guts to say it again, and not just because he had to save her, but because he wanted her to know how he felt.

"Mobius to Nate!"

He had been in such a daze that he didn't notice that they had reached the headquarters.

"Hurry up! The party's starting!"

He ran to catch up with her and they both walked inside, the door shutting behind them.

**THE END**

In the beginning I didn't think I would make it this far but it's nice to know that I got to the end. Thanks to everyone that bared with me during this story. Now that this is done I can start my new series, which is in fact a sequel to this story.

**near the end of the story where Alex says "Mobius to Nate", I noticed that I had at first written "Earth" and then realized that that was the wrong planet **


End file.
